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VS-1470 Have Extract Cohort to PGEN write to cost_observability table #8958

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merged 4 commits into from
Aug 21, 2024
Merged

VS-1470 Have Extract Cohort to PGEN write to cost_observability table #8958

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11f8dd1
Have ExtractCohortToPgen write to cost_observability table.
gbggrant Aug 19, 2024
bbf30ba
Update the gatk docker
gbggrant Aug 19, 2024
7e3ced5
Add more branches to .dockstore.yml
gbggrant Aug 19, 2024
4519501
Remove branches from .dockstore.yml
gbggrant Aug 21, 2024
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5 changes: 5 additions & 0 deletions .dockstore.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -290,6 +290,7 @@ workflows:
branches:
- master
- ah_var_store
- gg_VS-1470_HaveExtractCohortToPgenWriteToCOTable
tags:
- /.*/
- name: GvsQuickstartHailIntegration
Expand All @@ -299,6 +300,7 @@ workflows:
branches:
- master
- ah_var_store
- gg_VS-1470_HaveExtractCohortToPgenWriteToCOTable
tags:
- /.*/
- name: GvsQuickstartIntegration
Expand All @@ -309,6 +311,7 @@ workflows:
- master
- ah_var_store
- vs_1456_status_writes_bug
- gg_VS-1470_HaveExtractCohortToPgenWriteToCOTable
tags:
- /.*/
- name: GvsIngestTieout
Expand Down Expand Up @@ -429,6 +432,7 @@ workflows:
- master
- ah_var_store
- EchoCallset
- gg_VS-1470_HaveExtractCohortToPgenWriteToCOTable
- name: GvsExtractCallsetPgenMerged
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsExtractCallsetPgenMerged.wdl
Expand All @@ -438,6 +442,7 @@ workflows:
- ah_var_store
- EchoCallset
- rsa_vs_1441
- gg_VS-1470_HaveExtractCohortToPgenWriteToCOTable
- name: MergePgenHierarchicalWdl
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/MergePgenHierarchical.wdl
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsExtractCallsetPgen.wdl
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Expand Up @@ -441,7 +441,7 @@ task PgenExtractTask {
${FILTERING_ARGS} \
--dataset-id ~{dataset_name} \
--call-set-identifier ~{call_set_identifier} \
--wdl-step GvsExtractCallsetPgenPgen \
--wdl-step GvsExtractCallsetPgen \
--wdl-call PgenExtractTask \
--shard-identifier ~{interval_filename} \
~{cost_observability_line} \
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsUtils.wdl
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Expand Up @@ -74,7 +74,7 @@ task GetToolVersions {
String cloud_sdk_slim_docker = "gcr.io/google.com/cloudsdktool/cloud-sdk:435.0.0-slim"
String variants_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/variants:2024-08-15-alpine-254df9be288d"
String variants_nirvana_docker = "us.gcr.io/broad-dsde-methods/variantstore:nirvana_2022_10_19"
String gatk_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/gatk:2024_08_08-gatkbase-7dc245ec27ce"
String gatk_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/gatk:2024_08_19-gatkbase-cd5b6b7821b2"
String real_time_genomics_docker = "docker.io/realtimegenomics/rtg-tools:latest"
String gotc_imputation_docker = "us.gcr.io/broad-gotc-prod/imputation-bcf-vcf:1.0.5-1.10.2-0.1.16-1649948623"
String plink_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/plink2:2024-04-23-slim-a0a65f52cc0e"
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3 changes: 2 additions & 1 deletion src/main/java/org/broadinstitute/hellbender/tools/gvs/extract/ExtractCohortToPgen.java
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Expand Up @@ -211,7 +211,8 @@ protected void apply(VariantContext variantContext) {

@Override
public Object onTraversalSuccess() {
if(pgenWriter.getDroppedVariantCount() > 0l) {
super.onTraversalSuccess();
if (pgenWriter.getDroppedVariantCount() > 0l) {
logger.info(pgenWriter.getDroppedVariantCount() + " variants dropped by writer for exceeding the" +
" maximum number of allowed alt alleles.");
}
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